The molecular basis of somaclonal variation is not precisely known, but both genetic and epigenetic mechanisms have been proposed. The available evidence points toward the openUP (June 2007) existence of labile portions of the genome that can be modulated when the cells undergo the stress of tissue culture. Therefore, the hypothesis that there are identifiable and predictable DNA markers for the early diagnosis of somaclonal variation has been tested.Representational difference analysis was used to isolate unique fragments of DNA (difference products) between visible culture-induced off-type and normal banana plants.Markers generated from six difference products differentiated between some of the offtype and normal pairs. The genomic region around one of these difference products has been extensively characterized and has a high degree of polymorphism, with variation in up to 10% of the nucleotides sequenced in the region. This same region has been shown to vary in other pairs of off-type and normal banana plants derived from tissue culture as well as in plants propagated commercially in vitro. The data are consistent with the hypothesis that there is at least one particularly labile portion of the genome that is especially susceptible to the stress imposed during tissue culture and that is associated with higher rearrangement and mutation rates than other portions of the genome.Consequently, the regions that are reported here have the potential to be used as early detection tools for identifying somaclonal variants.
The amount, nature, and fate of DNA and protein in the major purification fractions generated during industrial scale refining of sugar cane into raw sugar by the diffuser and tandem roller mills was determined. The presence and size of sugar cane DNA were estimated using PCR and sugar cane specific primers that amplified fragments of various sizes from different segments of the repetitive intergenic region (IGS) of the 25S rDNA. Both the maximum fragment size capable of amplification and the amount of DNA decreased as refining progressed, indicating sequential degradation during the milling. However, PCR still detected minute quantities of sugar cane DNA in raw sugar (<10e-3 ppm). Using a bicinchoninic acid assay on trichloroacetic acid precipitated sodium dodecylsulfate-extracts, protein was found in all mill fractions and decreased from 4500 to 10 ppm as sugar cane was refined to raw sugar. Analysis of these extracts by one-and two-dimensional gel electrophoresis suggested a gradual degradation of proteins during refining. Shotgun proteomic analyses identified complex populations of sugar cane proteins, or peptides thereof, in all mill fractions, but the population complexity decreased during processing. Retail-purchased refined cane sugar showed no detectable protein or DNA (<2 ppm protein; 0.001 ppm DNA).
The highly repetitive sequences of the flax genome have been characterized. This has been done using a series of cloned probes that represent most, if not all, of the highly repetitive families in the flax genome. All of them are arranged as tandem arrays. The organization and copy number of these sequences has been compared in a number of lines including those lines (termed genotrophs) derived from the flax variety 'Stormont Cirrus' by the environmental induction of heritable changes, two other flax and linseed cultivars, and some of the supposed wild progenitors of flax. It was found that all except the light satellite differed in copy number between some of the lines. A particular subset of the 5S genes was shown to be preferentially affected when changes occurred. The extent of the variation between genotrophs was similar to that between different varieties or between flax and its supposed progenitor.Key words: flax, DNA variation, repeated sequences.
Tylosema esculentum (marama bean) is an important orphan legume from southern Africa that has long been considered to have the potential to be domesticated as a crop. The chloroplast genomes of 84 marama samples collected from various geographical locations in Namibia and Pretoria were compared in this study. The cp genomes were analyzed for diversity, including SNPs, indels, structural alterations, and heteroplasmy. The marama cp genomes ranged in length from 161,537 bp to 161,580 bp and contained the same sets of genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The genes rpoC2 and rpoB, and the intergenic spacers trnT-trnL and ndhG-ndhI were found to be more diverse than other regions of the marama plastome. 15 haplotypes were found to be divided into two groups, differing at 122 loci and at a 230 bp inversion. One type appears to have greater variability within the major genome present, and variations amongst individuals with this type of chloroplast genome seems to be distributed within specific geographic regions but with very limited sampling for some regions. However, deep sequencing has identified that within most of the individuals, both types of chloroplast genomes are present, albeit one is generally at a very low frequency. The inheritance of this complex of chloroplast genomes appears to be fairly constant, providing a conundrum of how the two genomes co-exist and are propagated through generations. The possible consequences for adaptation to the harsh environment in which T. esculentum survives are considered. The results pave the way for marama variety identification, as well as for understanding the origin and evolution of the bean.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
customersupport@researchsolutions.com
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
This site is protected by reCAPTCHA and the Google Privacy Policy and Terms of Service apply.
Copyright © 2025 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.